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云端基因组学
book

云端基因组学

by Geraldine A. Van der Auwera, Brian D. O’Connor
April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
China Electric Power Press Ltd.
Content preview from 云端基因组学
230
8
home
目录(而不是像前几章那样进入下级目录)运行命令,为了使各命令中所用路
径简短,我们新建一个变量,指向工作流文件所在路径:
$ export WF=~/book/code/workflows
最后我们来讨论文本编辑器。下面练习除一个之外,你将直接查看和运行我们预先
写好的脚本。下载或克隆这些文件到你的笔记本电脑,并用你最喜欢的文本编辑器
打开,就可以查看它们。但有个练习,我们建议你修改一处
WDL
,中断其运行,
查看
Cromwell
所抛错误信息,并学着处理类似行为,因此你需要实际编辑该文件。
我们介绍如何用
shell
的内置文本编辑器
nano
编辑文件,该编辑器被认为是最适合
不熟悉命令行文本编辑器的用户。你要是喜欢,当然还可以用
vi
emacs
shell
编辑器,如选用其他编辑器,请相应调整我们所提供的命令。
为开发
WDL
选一款文本编辑器
读完本书,在学习和工作中,如要编写或编辑自己的
WDL
文件,你可能会发
shell
命令行文本编辑器功能太有限。不管你喜欢用
IntelliJ
这类功能齐全的
集成开发环境(
IDE
)应用,还是
Sublime
这类带
GUI
的文本编辑器,你都
可以从这个在线文档(
https://oreil.ly/JSNo1
)找到几款推荐应用,它们兼容
WDL
句法突出显示插件。请注意,每次你都需要将自己在本地机器上编辑过
的代码回传虚拟机,再试运行它们。或者,你可以在本地测试代码(
Cromwell
可以在你的台式机上运行),只有处理大规模任务,再上云。
WDL
开发还可以用第
4
章介绍的
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Publisher Resources

ISBN: 9787519864422